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Hyperontology for the Biomedical OntologistA Sketch and Some Examples
Oliver Kutz 1
Till Mossakowski 1, 2
Janna Hastings 3,4
Alexander Garcia Castro 5
Aleksandra Sojic 6
1 Research Center on Spatial Cognition, University of Bremen, Germany2 DFKI GmbH Bremen and University of Bremen, Germany
3 Chemoinformatics and Metabolism, European Bioinformatics Institute, UK4 Swiss Centre for Affective Sciences, University of Geneva, Switzerland
5 University of Arkansas for Medical Sciences, USA6 European School of Molecular Medicine, Milan; and University of Milan, Italy
ICBO, Buffalo, July 2011
Wednesday, April 12, 2023 2
Heterogeneous Formalisms
Hyperontology for Bio-ontologists (WoMBO @ ICBO 2011)
OWL
OBOHOL
CL RDF
RulesFrames
OWL-EL
OWL-RL
Modal logic Temporal logic
Fuzzy logicNon-monotonic
logic
Wednesday, April 12, 2023 3Hyperontology for Bio-ontologists (WoMBO @ ICBO 2011)
Wednesday, April 12, 2023 4
Heterogeneous Content
Hyperontology for Bio-ontologists (WoMBO @ ICBO 2011)
Patient information
agefamily history
Disease information
social status
Physiological information
diet
blood pressuremetabolic profile
genotype
cell type
pathways
etiology
symptomsGranularity
Time Qualitative /Quantative
Pathological / Canonical
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Modularity as desiderataSmall modules:• human understandable, re-usable, one level at
a time, etc.• Proving-in-the-small
Large programs constructed from modules:• Composition, Linkage, etc.• Proving-in-the-large
Idea of a Module Interconnection Language
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Modularity at design-time
Subject-specific modules
Logic-specific modules (extensions)
“Minimal” expressivity for a given topic
Imports and complex interrelationships
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Hyperontology is a framework for interrelating
heterogeneous ontologymodules
Hyperontology for Bio-ontologists (WoMBO @ ICBO 2011)
Logical translation
Modular connections
Integrated tools and reasoners
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Systematically linking ontology modules defined in different formalisms requires:
A logic graph
Fixed logic translations
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Common Algebraic Specification Language
Standardised many-sorted first-order specification language
Various extensions and sublanguages, including higher-order dialects, modal logic, OWL-DL;
Supports structured specifications including: imports, hiding, renaming, union, extensions.
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Semantics of structured specifications
Wednesday, April 12, 2023 11Hyperontology for Bio-ontologists (WoMBO @ ICBO 2011)
HETCASL
Extension of CASL for seamless combination of different logics
Provides syntactic “sugar”
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HETS – The Heterogeneous Tool SetStructured representations
Reuse/independent development of modules
Library of logics/formalisms supported, incl. OWL-DL
Various provers connected: incl. OWLDL, first-order, higher-order, model checker
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Wednesday, April 12, 2023 14Hyperontology for Bio-ontologists (WoMBO @ ICBO 2011)
Applications
A sketch of some scenarios
from bio-ontologies
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HOL as constraintBoth the Sequence Ontology (SO) and the RNAO
provide axiomatizations in first-order and higher-order logic
to further constrain the semantics of the relationships that they use in OWL
(not explicitly linked to the OWL version)
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SIMULATION
ANATOMY
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Biochemical Structures
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FullerenesCubic, 3-connected, planar graphs in which all faces are either pentagons or hexagons (5 or 6 atoms).
Can be defined with Monadic Second Order Logic (MSOL)
Cubic
3-connected
Planar (Kuratowski)
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Interrelating Ontologies
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Wednesday, April 12, 2023 21Hyperontology for Bio-ontologists (WoMBO @ ICBO 2011)
Conclusions
Biomedical ontologies are highly complex
and need diverse formalisms for proper treatment
The Hyperontology framework provides the “plumbing” to seamlessly integrate such
formalisms
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Acknowledgements
FundingDFG-funded collaborative research centre
SFB/TR 8 `Spatial Cognition' The German Federal Ministry of Education and
Research (Project 01 IW 07002 FormalSafe).